Nearly all 22,537 civil servants in Northern Ireland received pay rises between 2012 and 2013 as a settlement of equal pay claims kicked in.
According to the Northern Ireland Statistics and Research Agency (Nisra) report, 93% of civil servants received pay increases in 2012/13.
Those in the clerical posts of administrative assistants and administrative officers won pay rises of up to 40%, earning more than their counterparts in England, Scotland and Wales.
And at the top of the ladder, there are now 16 people earning over £100,000, a category which includes permanent secretaries who lead government departments.
The pay increases come during continued austerity in the private sector, where employees of many companies in the public sector have seen five years of pay freezes.
Jonathan Isaby, political director of the TaxPayers' Alliance, said: "At a time when budgets are so tight and wages stagnating, the taxpayers footing the bills will rightly be surprised at the pay rises that have been enjoyed by so many Northern Ireland Civil Service staff.
"Given that civil servants already enjoy far better pay and pensions than their private sector counterparts and the fact that the nation's finances remain in a dire state, public sector pay needs to be kept under control – especially when so many families are struggling to make ends meet."
The amount of pay increases varied. Just under three quarters of middle managers at the higher executive officer level, just over 40% of those at lower executive officer level, and 29% of senior civil service staff received increases of 6% or more.
Nisra's report said the increases were down to new pay scales introduced following a pay and grading review and a reform of civil service pay.
But Kieran Bannon, assistant general secretary of public sector union Nipsa, said it did not believe the pay increases to be excessive, and said the pay scales had been negotiated following equal pay cases brought by the union in 2009.
"We do not see them as excessive, not in the context of equal pay within the Northern Ireland Civil Service," he said.
The average civil service salary in Northern Ireland is just under £23,999, according to Nisra's report. The bottom 10% earn £18,000 and the top 10% earn a basic salary of £39,300.
But the pay increases were not applied across the board, and did not include prison staff, around 40% of administrative assistants and just over a quarter of top-ranking staff in grade six.
UKIP MLA David McNarry said: "I think the civil servants have to recognise how good they have had it. They have been on an offensive about their pay over the last three years, but the evidence which these figures show makes that all ring hollow."